I tested out the newest Snapshot with a copy of my World and noticed that a Chunk got completly regenerated.
After some testing I found the Problem:

1. Create a new creative World in 1.6.4
2. Give yourself a Nether Wart (ID 115 in my World, seems to have got another ID since I placed it) and an Item Frame
3. Place the Nether Wart in the Item Frame
4. Load the World in the current Snapshot, the Chunk will be replaced.

If you try to give yourself the Item 115 in the Snapshot the Game will crash.

My guess is that the Nether Wart is supposed to be replaced by the new ID on updating, but it does not work with Items in Item Frames.